Starting phenix.real_space_refine on Thu Aug 6 15:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy5_37916/08_2026/8wy5_37916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy5_37916/08_2026/8wy5_37916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wy5_37916/08_2026/8wy5_37916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy5_37916/08_2026/8wy5_37916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wy5_37916/08_2026/8wy5_37916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy5_37916/08_2026/8wy5_37916.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 76 5.49 5 S 48 5.16 5 C 10048 2.51 5 N 2664 2.21 5 O 3198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "B" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "C" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3598 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 8, 'TRANS': 431} Chain breaks: 2 Chain: "D" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3640 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "H" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.11, per 1000 atoms: 0.19 Number of scatterers: 16038 At special positions: 0 Unit cell: (118.44, 78.96, 185.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 48 16.00 P 76 15.00 O 3198 8.00 N 2664 7.00 C 10048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 507.9 milliseconds 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3356 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 16 sheets defined 38.5% alpha, 15.3% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.889A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.687A pdb=" N PHE A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.713A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.632A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.633A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.723A pdb=" N TYR A 398 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU A 399 " --> pdb=" O PRO A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.639A pdb=" N CYS A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.628A pdb=" N LEU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 512 through 529 removed outlier: 3.626A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ARG A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.537A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.572A pdb=" N VAL A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.542A pdb=" N GLU A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.749A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.857A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 380 through 395 removed outlier: 4.130A pdb=" N LYS B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 removed outlier: 4.062A pdb=" N LEU B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 removed outlier: 4.429A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.568A pdb=" N LEU B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.622A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 511 through 518 removed outlier: 3.646A pdb=" N ASP B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.718A pdb=" N LYS B 539 " --> pdb=" O HIS B 535 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.954A pdb=" N LYS B 570 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.798A pdb=" N PHE C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 83 through 94 removed outlier: 4.187A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.763A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.761A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.723A pdb=" N PHE C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 372 " --> pdb=" O ALA C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 380 through 391 removed outlier: 3.521A pdb=" N ILE C 385 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.665A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 402 " --> pdb=" O TYR C 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 402' Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.779A pdb=" N CYS C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.993A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 457 " --> pdb=" O CYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.675A pdb=" N ARG C 481 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 482 " --> pdb=" O LYS C 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 501 removed outlier: 4.152A pdb=" N GLU C 499 " --> pdb=" O ASN C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.697A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.160A pdb=" N ILE C 527 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.622A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C 539 " --> pdb=" O HIS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.625A pdb=" N LEU C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.793A pdb=" N VAL C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.925A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 83 through 91 removed outlier: 4.059A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.847A pdb=" N ALA D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.697A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 3.545A pdb=" N ALA D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.826A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 385 " --> pdb=" O PRO D 381 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 391 " --> pdb=" O PHE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 424 removed outlier: 3.516A pdb=" N CYS D 418 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 4.056A pdb=" N LEU D 456 " --> pdb=" O ARG D 452 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 457 " --> pdb=" O CYS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 4.009A pdb=" N LYS D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 484 " --> pdb=" O GLU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 501 removed outlier: 4.088A pdb=" N GLU D 499 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 516 removed outlier: 3.872A pdb=" N ASP D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 523 through 529 removed outlier: 4.029A pdb=" N ILE D 527 " --> pdb=" O SER D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 4.014A pdb=" N LYS D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 removed outlier: 3.799A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 540 through 546' Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 566 through 574 removed outlier: 3.823A pdb=" N LYS D 570 " --> pdb=" O PHE D 566 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 573 " --> pdb=" O LEU D 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.975A pdb=" N VAL A 17 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 8 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 71 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.149A pdb=" N LYS A 150 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 286 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 152 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLU A 288 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 154 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 7.011A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR A 506 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 429 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.650A pdb=" N VAL B 17 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 8 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 71 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.526A pdb=" N TYR B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.613A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 375 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR B 506 " --> pdb=" O HIS B 427 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 429 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER B 508 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR B 431 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.943A pdb=" N VAL C 17 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 8 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 71 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.326A pdb=" N LYS C 150 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 286 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 152 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLU C 288 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 154 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 25 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 335 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 403 through 407 removed outlier: 7.006A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.906A pdb=" N VAL D 17 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 8 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 71 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 149 through 154 removed outlier: 8.501A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 403 through 407 Processing sheet with id=AB7, first strand: chain 'D' and resid 435 through 437 434 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3709 1.33 - 1.45: 3501 1.45 - 1.57: 9018 1.57 - 1.69: 160 1.69 - 1.81: 76 Bond restraints: 16464 Sorted by residual: bond pdb=" C3' DT F 6 " pdb=" O3' DT F 6 " ideal model delta sigma weight residual 1.435 1.498 -0.063 1.30e-02 5.92e+03 2.32e+01 bond pdb=" C3' DT H 6 " pdb=" O3' DT H 6 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.19e+01 bond pdb=" C1' DC E 10 " pdb=" N1 DC E 10 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" C3' DT G 14 " pdb=" O3' DT G 14 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C3' DT E 14 " pdb=" O3' DT E 14 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.38e+01 ... (remaining 16459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 21638 2.71 - 5.42: 641 5.42 - 8.14: 101 8.14 - 10.85: 62 10.85 - 13.56: 8 Bond angle restraints: 22450 Sorted by residual: angle pdb=" C LEU B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 121.54 134.94 -13.40 1.91e+00 2.74e-01 4.92e+01 angle pdb=" C GLU A 471 " pdb=" N ASP A 472 " pdb=" CA ASP A 472 " ideal model delta sigma weight residual 121.54 134.15 -12.61 1.91e+00 2.74e-01 4.36e+01 angle pdb=" C GLU C 471 " pdb=" N ASP C 472 " pdb=" CA ASP C 472 " ideal model delta sigma weight residual 121.54 134.12 -12.58 1.91e+00 2.74e-01 4.34e+01 angle pdb=" C ASP A 64 " pdb=" N THR A 65 " pdb=" CA THR A 65 " ideal model delta sigma weight residual 121.54 133.96 -12.42 1.91e+00 2.74e-01 4.23e+01 angle pdb=" C LYS B 341 " pdb=" N VAL B 342 " pdb=" CA VAL B 342 " ideal model delta sigma weight residual 121.97 132.81 -10.84 1.80e+00 3.09e-01 3.63e+01 ... (remaining 22445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 9368 34.89 - 69.79: 455 69.79 - 104.68: 15 104.68 - 139.58: 0 139.58 - 174.47: 6 Dihedral angle restraints: 9844 sinusoidal: 4650 harmonic: 5194 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASP C 515 " pdb=" C ASP C 515 " pdb=" N LEU C 516 " pdb=" CA LEU C 516 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 9841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2411 0.140 - 0.280: 86 0.280 - 0.419: 5 0.419 - 0.559: 2 0.559 - 0.699: 6 Chirality restraints: 2510 Sorted by residual: chirality pdb=" CB VAL B 342 " pdb=" CA VAL B 342 " pdb=" CG1 VAL B 342 " pdb=" CG2 VAL B 342 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" P DA H 20 " pdb=" OP1 DA H 20 " pdb=" OP2 DA H 20 " pdb=" O5' DA H 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" P DA F 20 " pdb=" OP1 DA F 20 " pdb=" OP2 DA F 20 " pdb=" O5' DA F 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 2507 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 93 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C VAL B 93 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL B 93 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS B 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 395 " 0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO D 396 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 396 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 396 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 520 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ILE B 520 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE B 520 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 521 " -0.015 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5256 2.88 - 3.39: 12922 3.39 - 3.89: 26558 3.89 - 4.40: 29956 4.40 - 4.90: 49730 Nonbonded interactions: 124422 Sorted by model distance: nonbonded pdb=" O ASP C 32 " pdb=" OG1 THR C 36 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR B 153 " pdb=" OE1 GLU B 288 " model vdw 2.385 3.040 nonbonded pdb=" OG SER D 78 " pdb=" O ALA D 102 " model vdw 2.389 3.040 nonbonded pdb=" O ASP A 32 " pdb=" OG1 THR A 36 " model vdw 2.389 3.040 nonbonded pdb=" O ASP B 32 " pdb=" OG1 THR B 36 " model vdw 2.396 3.040 ... (remaining 124417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 351 or resid 363 through 1001)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 351 or resid 363 through 1001)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 16464 Z= 0.419 Angle : 1.202 13.561 22450 Z= 0.720 Chirality : 0.071 0.699 2510 Planarity : 0.006 0.081 2586 Dihedral : 18.379 174.473 6488 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.04 % Favored : 94.50 % Rotamer: Outliers : 0.18 % Allowed : 0.67 % Favored : 99.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.15), residues: 1746 helix: -4.48 (0.08), residues: 532 sheet: -0.56 (0.27), residues: 356 loop : -2.38 (0.16), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 12 TYR 0.031 0.002 TYR D 113 PHE 0.035 0.003 PHE C 387 TRP 0.018 0.003 TRP B 126 HIS 0.005 0.001 HIS C 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.42 (16464) covalent geometry : angle 1.20241 / 0.72 (22450) hydrogen bonds : bond 0.22568 / 15.01 ( 516) hydrogen bonds : angle 8.94462 / 6.23 ( 1391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5466 (t80) cc_final: 0.4895 (t80) REVERT: A 367 SER cc_start: 0.8211 (m) cc_final: 0.7982 (p) REVERT: A 388 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6356 (mt-10) REVERT: A 507 LEU cc_start: 0.7896 (tp) cc_final: 0.7593 (tp) REVERT: B 1 MET cc_start: 0.4486 (mtp) cc_final: 0.3440 (tmm) REVERT: B 105 PHE cc_start: 0.4023 (t80) cc_final: 0.1745 (t80) REVERT: B 493 TYR cc_start: 0.7744 (m-80) cc_final: 0.7489 (m-80) REVERT: B 507 LEU cc_start: 0.7356 (tp) cc_final: 0.7116 (tp) REVERT: C 2 LYS cc_start: 0.6309 (ptpt) cc_final: 0.6103 (pptt) REVERT: C 106 TYR cc_start: 0.6638 (m-80) cc_final: 0.6419 (m-80) REVERT: C 388 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7139 (mt-10) REVERT: C 550 ASN cc_start: 0.6972 (m-40) cc_final: 0.6358 (p0) REVERT: C 571 GLU cc_start: 0.6415 (mp0) cc_final: 0.5812 (mp0) REVERT: D 141 ASN cc_start: 0.7895 (m-40) cc_final: 0.7675 (m110) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.1198 time to fit residues: 49.2647 Evaluate side-chains 166 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN B 563 HIS C 13 ASN D 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.253771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.206846 restraints weight = 18913.913| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.56 r_work: 0.4062 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16464 Z= 0.168 Angle : 0.686 9.011 22450 Z= 0.381 Chirality : 0.050 0.334 2510 Planarity : 0.004 0.049 2586 Dihedral : 20.122 174.639 2759 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.93 % Favored : 94.67 % Rotamer: Outliers : 0.67 % Allowed : 7.85 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.17), residues: 1746 helix: -2.83 (0.16), residues: 514 sheet: -0.33 (0.28), residues: 356 loop : -2.00 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 481 TYR 0.024 0.002 TYR B 113 PHE 0.017 0.002 PHE B 11 TRP 0.007 0.002 TRP B 126 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (16464) covalent geometry : angle 0.68604 / 0.38 (22450) hydrogen bonds : bond 0.06003 / 3.88 ( 516) hydrogen bonds : angle 6.42237 / 4.47 ( 1391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5513 (t80) cc_final: 0.5136 (t80) REVERT: A 117 GLU cc_start: 0.6388 (tp30) cc_final: 0.6126 (tp30) REVERT: A 388 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6698 (mt-10) REVERT: A 492 GLN cc_start: 0.8010 (pp30) cc_final: 0.7750 (pp30) REVERT: B 1 MET cc_start: 0.3960 (mtp) cc_final: 0.3049 (tpt) REVERT: B 507 LEU cc_start: 0.7650 (tp) cc_final: 0.7437 (tp) REVERT: C 296 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6162 (mtm180) REVERT: C 545 MET cc_start: 0.6817 (mmt) cc_final: 0.6169 (mmt) REVERT: C 571 GLU cc_start: 0.6512 (mp0) cc_final: 0.6012 (mp0) REVERT: D 132 ASN cc_start: 0.6791 (t0) cc_final: 0.6582 (t0) REVERT: D 143 ASN cc_start: 0.5975 (m110) cc_final: 0.5772 (m-40) REVERT: D 509 GLU cc_start: 0.6338 (pm20) cc_final: 0.6080 (pm20) outliers start: 11 outliers final: 5 residues processed: 205 average time/residue: 0.1160 time to fit residues: 35.1328 Evaluate side-chains 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 150 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 415 HIS B 421 ASN B 544 ASN C 132 ASN C 535 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.250654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.209893 restraints weight = 19024.467| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.21 r_work: 0.4083 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16464 Z= 0.135 Angle : 0.602 8.034 22450 Z= 0.338 Chirality : 0.048 0.360 2510 Planarity : 0.003 0.038 2586 Dihedral : 20.054 176.124 2759 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.21 % Favored : 94.44 % Rotamer: Outliers : 0.80 % Allowed : 11.96 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.18), residues: 1746 helix: -1.70 (0.20), residues: 528 sheet: -0.41 (0.28), residues: 376 loop : -1.75 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 374 TYR 0.016 0.001 TYR D 113 PHE 0.014 0.001 PHE D 316 TRP 0.004 0.002 TRP B 126 HIS 0.007 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (16464) covalent geometry : angle 0.60187 / 0.34 (22450) hydrogen bonds : bond 0.04695 / 3.00 ( 516) hydrogen bonds : angle 5.86159 / 4.09 ( 1391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4715 (tpt) cc_final: 0.4369 (tpt) REVERT: A 105 PHE cc_start: 0.5465 (t80) cc_final: 0.5223 (t80) REVERT: A 388 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6734 (mt-10) REVERT: A 481 ARG cc_start: 0.8737 (mtp85) cc_final: 0.8201 (mtp180) REVERT: A 524 MET cc_start: 0.5978 (mtt) cc_final: 0.5710 (mmm) REVERT: B 1 MET cc_start: 0.3738 (mtp) cc_final: 0.3013 (tpt) REVERT: B 481 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7946 (ptt180) REVERT: C 87 LYS cc_start: 0.6574 (mmtt) cc_final: 0.5272 (mttp) REVERT: D 143 ASN cc_start: 0.5823 (m110) cc_final: 0.5620 (m-40) REVERT: D 392 ASP cc_start: 0.7072 (t0) cc_final: 0.6843 (t0) REVERT: D 566 PHE cc_start: 0.7860 (m-80) cc_final: 0.7495 (m-10) outliers start: 13 outliers final: 9 residues processed: 185 average time/residue: 0.1164 time to fit residues: 32.2101 Evaluate side-chains 162 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 432 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 1 optimal weight: 0.0870 chunk 115 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN C 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.249833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.207620 restraints weight = 18889.922| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.43 r_work: 0.4061 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16464 Z= 0.128 Angle : 0.581 8.001 22450 Z= 0.326 Chirality : 0.048 0.355 2510 Planarity : 0.003 0.029 2586 Dihedral : 19.880 175.746 2759 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.33 % Favored : 94.33 % Rotamer: Outliers : 0.86 % Allowed : 13.25 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.19), residues: 1746 helix: -1.09 (0.22), residues: 528 sheet: -0.35 (0.28), residues: 376 loop : -1.50 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 504 TYR 0.023 0.001 TYR A 493 PHE 0.015 0.001 PHE D 105 TRP 0.004 0.001 TRP B 126 HIS 0.003 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (16464) covalent geometry : angle 0.58147 / 0.33 (22450) hydrogen bonds : bond 0.04271 / 2.70 ( 516) hydrogen bonds : angle 5.58451 / 3.90 ( 1391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4492 (tpt) cc_final: 0.4268 (tpt) REVERT: A 388 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6670 (mt-10) REVERT: A 524 MET cc_start: 0.6050 (mtt) cc_final: 0.5760 (mmm) REVERT: A 563 HIS cc_start: 0.4239 (OUTLIER) cc_final: 0.3808 (m90) REVERT: B 1 MET cc_start: 0.3647 (mtp) cc_final: 0.2973 (tpt) REVERT: B 481 ARG cc_start: 0.8324 (mtm180) cc_final: 0.7990 (ptt180) REVERT: C 87 LYS cc_start: 0.6636 (mmtt) cc_final: 0.5323 (mttp) REVERT: D 143 ASN cc_start: 0.5839 (m110) cc_final: 0.5635 (m-40) REVERT: D 392 ASP cc_start: 0.7147 (t0) cc_final: 0.6887 (t0) REVERT: D 566 PHE cc_start: 0.7910 (m-80) cc_final: 0.7618 (m-10) outliers start: 14 outliers final: 10 residues processed: 182 average time/residue: 0.1096 time to fit residues: 29.9424 Evaluate side-chains 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 314 TYR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 345 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 126 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.247699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.203795 restraints weight = 18929.358| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.39 r_work: 0.4020 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16464 Z= 0.139 Angle : 0.588 8.120 22450 Z= 0.326 Chirality : 0.047 0.356 2510 Planarity : 0.003 0.030 2586 Dihedral : 19.784 175.156 2759 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.33 % Favored : 94.33 % Rotamer: Outliers : 1.29 % Allowed : 14.85 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1746 helix: -0.70 (0.22), residues: 534 sheet: -0.45 (0.28), residues: 370 loop : -1.33 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 12 TYR 0.019 0.001 TYR C 106 PHE 0.013 0.001 PHE A 315 TRP 0.005 0.002 TRP B 126 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (16464) covalent geometry : angle 0.58778 / 0.33 (22450) hydrogen bonds : bond 0.04243 / 2.67 ( 516) hydrogen bonds : angle 5.45933 / 3.82 ( 1391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6691 (mt-10) REVERT: A 563 HIS cc_start: 0.4363 (OUTLIER) cc_final: 0.3835 (m90) REVERT: B 1 MET cc_start: 0.3729 (mtp) cc_final: 0.3140 (tpt) REVERT: B 481 ARG cc_start: 0.8402 (mtm180) cc_final: 0.8042 (ptt180) REVERT: B 504 ARG cc_start: 0.7246 (mmm-85) cc_final: 0.6550 (mmt180) REVERT: C 87 LYS cc_start: 0.6707 (mmtt) cc_final: 0.5414 (mttp) REVERT: C 125 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6948 (mtpp) REVERT: D 143 ASN cc_start: 0.6012 (m110) cc_final: 0.5779 (m-40) REVERT: D 566 PHE cc_start: 0.7885 (m-80) cc_final: 0.7563 (m-10) outliers start: 21 outliers final: 10 residues processed: 178 average time/residue: 0.1323 time to fit residues: 35.6379 Evaluate side-chains 161 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 439 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN C 483 ASN C 550 ASN D 421 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.247107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.204312 restraints weight = 18817.328| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.31 r_work: 0.4044 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16464 Z= 0.136 Angle : 0.586 8.367 22450 Z= 0.323 Chirality : 0.047 0.353 2510 Planarity : 0.003 0.029 2586 Dihedral : 19.725 175.067 2758 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.38 % Favored : 94.27 % Rotamer: Outliers : 0.86 % Allowed : 16.38 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.19), residues: 1746 helix: -0.56 (0.23), residues: 530 sheet: -0.36 (0.28), residues: 366 loop : -1.28 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 12 TYR 0.013 0.001 TYR C 106 PHE 0.014 0.001 PHE A 315 TRP 0.004 0.002 TRP B 126 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (16464) covalent geometry : angle 0.58577 / 0.32 (22450) hydrogen bonds : bond 0.04120 / 2.59 ( 516) hydrogen bonds : angle 5.40828 / 3.78 ( 1391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6659 (mt-10) REVERT: A 563 HIS cc_start: 0.4224 (OUTLIER) cc_final: 0.3710 (m90) REVERT: B 1 MET cc_start: 0.3670 (mtp) cc_final: 0.3169 (tpt) REVERT: B 504 ARG cc_start: 0.7286 (mmm-85) cc_final: 0.6590 (mmt180) REVERT: C 87 LYS cc_start: 0.6693 (mmtt) cc_final: 0.5415 (mttp) REVERT: D 143 ASN cc_start: 0.5966 (m110) cc_final: 0.5765 (m-40) REVERT: D 566 PHE cc_start: 0.7954 (m-80) cc_final: 0.7643 (m-10) outliers start: 14 outliers final: 12 residues processed: 169 average time/residue: 0.1279 time to fit residues: 32.7609 Evaluate side-chains 163 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 140 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 330 ASN D 350 ASN D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.246947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.204086 restraints weight = 18700.753| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.43 r_work: 0.4031 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16464 Z= 0.130 Angle : 0.575 7.997 22450 Z= 0.320 Chirality : 0.047 0.351 2510 Planarity : 0.003 0.047 2586 Dihedral : 19.660 175.012 2758 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.50 % Favored : 94.16 % Rotamer: Outliers : 1.04 % Allowed : 16.93 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1746 helix: -0.41 (0.23), residues: 530 sheet: -0.36 (0.28), residues: 366 loop : -1.20 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 504 TYR 0.012 0.001 TYR D 536 PHE 0.013 0.001 PHE A 315 TRP 0.004 0.001 TRP D 126 HIS 0.010 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (16464) covalent geometry : angle 0.57518 / 0.32 (22450) hydrogen bonds : bond 0.03997 / 2.51 ( 516) hydrogen bonds : angle 5.33665 / 3.73 ( 1391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6697 (mt-10) REVERT: A 481 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8215 (mtp180) REVERT: A 563 HIS cc_start: 0.4222 (OUTLIER) cc_final: 0.3694 (m90) REVERT: B 1 MET cc_start: 0.3588 (mtp) cc_final: 0.3161 (tpt) REVERT: B 504 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.6692 (mmt180) REVERT: C 87 LYS cc_start: 0.6705 (mmtt) cc_final: 0.5430 (mttp) REVERT: C 524 MET cc_start: 0.6177 (mtt) cc_final: 0.5895 (mmm) REVERT: D 143 ASN cc_start: 0.5938 (m110) cc_final: 0.5725 (m-40) REVERT: D 566 PHE cc_start: 0.7971 (m-80) cc_final: 0.7689 (m-10) outliers start: 17 outliers final: 14 residues processed: 168 average time/residue: 0.1166 time to fit residues: 30.0492 Evaluate side-chains 164 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN D 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.244045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.201028 restraints weight = 18685.980| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.28 r_work: 0.3984 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16464 Z= 0.179 Angle : 0.630 9.795 22450 Z= 0.346 Chirality : 0.049 0.349 2510 Planarity : 0.003 0.044 2586 Dihedral : 19.696 174.567 2758 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.01 % Favored : 93.64 % Rotamer: Outliers : 1.60 % Allowed : 16.81 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1746 helix: -0.47 (0.23), residues: 546 sheet: -0.44 (0.28), residues: 362 loop : -1.27 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 12 TYR 0.016 0.002 TYR C 106 PHE 0.016 0.002 PHE A 315 TRP 0.007 0.002 TRP D 126 HIS 0.008 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (16464) covalent geometry : angle 0.63047 / 0.35 (22450) hydrogen bonds : bond 0.04419 / 2.79 ( 516) hydrogen bonds : angle 5.44835 / 3.81 ( 1391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6761 (mt-10) REVERT: A 481 ARG cc_start: 0.8792 (mtp85) cc_final: 0.8243 (mtp180) REVERT: A 563 HIS cc_start: 0.4363 (OUTLIER) cc_final: 0.3665 (m90) REVERT: B 1 MET cc_start: 0.3477 (mtp) cc_final: 0.3190 (tpt) REVERT: B 504 ARG cc_start: 0.7293 (mmm-85) cc_final: 0.6672 (mmt180) REVERT: C 87 LYS cc_start: 0.6763 (mmtt) cc_final: 0.5503 (mttp) REVERT: C 284 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7469 (mt) REVERT: C 296 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.5859 (mtm180) REVERT: C 510 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7085 (pt) REVERT: C 524 MET cc_start: 0.6232 (mtt) cc_final: 0.5959 (mmm) outliers start: 26 outliers final: 16 residues processed: 182 average time/residue: 0.1141 time to fit residues: 31.5190 Evaluate side-chains 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 344 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.0000 chunk 177 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 ASN D 330 ASN D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.246215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.199407 restraints weight = 18728.134| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.75 r_work: 0.3927 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16464 Z= 0.158 Angle : 0.617 9.967 22450 Z= 0.339 Chirality : 0.048 0.349 2510 Planarity : 0.003 0.043 2586 Dihedral : 19.682 174.349 2758 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.04 % Rotamer: Outliers : 1.41 % Allowed : 17.42 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1746 helix: -0.44 (0.22), residues: 558 sheet: -0.45 (0.28), residues: 362 loop : -1.19 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 12 TYR 0.014 0.001 TYR D 106 PHE 0.016 0.001 PHE A 315 TRP 0.005 0.002 TRP B 126 HIS 0.005 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (16464) covalent geometry : angle 0.61659 / 0.34 (22450) hydrogen bonds : bond 0.04201 / 2.66 ( 516) hydrogen bonds : angle 5.40845 / 3.78 ( 1391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6696 (mt-10) REVERT: A 481 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8296 (mtp180) REVERT: A 563 HIS cc_start: 0.4229 (OUTLIER) cc_final: 0.3511 (m90) REVERT: B 1 MET cc_start: 0.3509 (mtp) cc_final: 0.3210 (tpt) REVERT: B 504 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6720 (mmt180) REVERT: C 87 LYS cc_start: 0.6887 (mmtt) cc_final: 0.5485 (mttp) REVERT: C 125 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6914 (mtpp) REVERT: C 510 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.7005 (pt) REVERT: C 524 MET cc_start: 0.6181 (mtt) cc_final: 0.5902 (mmm) REVERT: D 284 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7455 (mt) outliers start: 23 outliers final: 16 residues processed: 175 average time/residue: 0.1221 time to fit residues: 32.7160 Evaluate side-chains 172 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 105 PHE Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 105 PHE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 77 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN B 421 ASN D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.245302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.202352 restraints weight = 18729.809| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.35 r_work: 0.4013 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16464 Z= 0.127 Angle : 0.587 9.306 22450 Z= 0.324 Chirality : 0.047 0.347 2510 Planarity : 0.003 0.083 2586 Dihedral : 19.616 174.593 2758 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 0.98 % Allowed : 17.73 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1746 helix: -0.31 (0.23), residues: 558 sheet: -0.44 (0.28), residues: 366 loop : -1.06 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 452 TYR 0.013 0.001 TYR D 106 PHE 0.014 0.001 PHE A 315 TRP 0.005 0.001 TRP B 126 HIS 0.005 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (16464) covalent geometry : angle 0.58717 / 0.32 (22450) hydrogen bonds : bond 0.03887 / 2.45 ( 516) hydrogen bonds : angle 5.28020 / 3.69 ( 1391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ARG cc_start: 0.8769 (mtp85) cc_final: 0.8278 (mtp180) REVERT: A 563 HIS cc_start: 0.4378 (OUTLIER) cc_final: 0.3721 (m90) REVERT: B 1 MET cc_start: 0.3470 (mtp) cc_final: 0.3183 (tpt) REVERT: B 504 ARG cc_start: 0.7204 (mmm-85) cc_final: 0.6750 (mmt180) REVERT: C 87 LYS cc_start: 0.6833 (mmtt) cc_final: 0.5516 (mttp) REVERT: C 125 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6836 (mtpp) REVERT: C 510 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.7061 (pt) REVERT: C 524 MET cc_start: 0.6175 (mtt) cc_final: 0.5918 (mmm) outliers start: 16 outliers final: 13 residues processed: 168 average time/residue: 0.1164 time to fit residues: 30.0113 Evaluate side-chains 164 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 123 optimal weight: 0.0010 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN D 330 ASN D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.243564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.200164 restraints weight = 18648.481| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.40 r_work: 0.3987 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16464 Z= 0.154 Angle : 0.619 10.235 22450 Z= 0.339 Chirality : 0.048 0.346 2510 Planarity : 0.003 0.075 2586 Dihedral : 19.593 174.451 2758 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.13 % Favored : 93.47 % Rotamer: Outliers : 1.10 % Allowed : 17.61 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1746 helix: -0.27 (0.23), residues: 558 sheet: -0.42 (0.28), residues: 362 loop : -1.09 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 504 TYR 0.016 0.001 TYR A 536 PHE 0.015 0.001 PHE A 315 TRP 0.005 0.002 TRP D 126 HIS 0.004 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16464) covalent geometry : angle 0.61931 / 0.34 (22450) hydrogen bonds : bond 0.04138 / 2.60 ( 516) hydrogen bonds : angle 5.34100 / 3.74 ( 1391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3254.30 seconds wall clock time: 56 minutes 41.44 seconds (3401.44 seconds total)